Unless a penis is present, most intersex babies are assigned female because it is not possible to construct a fully functional penis. The gender assignment and the surgery are usually done immediately after birth, with possible additional surgery after puberty. Today, some physicians such as Eric Vilain (featured in the video) recommend allowing the child to make his or her own surgical decisions later in life. However, most parents choose the surgery earlier because they are uncomfortable with the ambiguity.

The Intersex Society of North America believes that intersex is not an abnormality but rather "an anatomical variation from the standard male and female types."3 The Society also believes that the decision regarding treatment, if any, should be made by the individual when he or she is capable of informed consent. The Society has two objections to treatment: 1) treatment assumes that intersexuality is a disease, and 2) surgery often damages sexual function, while still failing to produce anatomically normal genitals. They claim that physicians have traditionally failed to communicate to parents the basis for the assignment of gender, which is not always (and in the case of XY individuals without a penis, never) made based on biological sex. They also claim that some physicians have failed to inform parents of alternatives and presented elective surgery as essential for health.

Physicians were once guided by the idea that infants are gender neutral at birth, and that normal gender development would follow from the environment of the child based on the sex assigned to the child.4 They believed that gender came from "nurture" rather than "nature." In recent years individuals, especially intersexuals, have protested that the environment does not control gender and, given that the treatments are irreversible, they should be delayed until the child determines his or her true gender. Others worry, however, that children with ambiguous genitals will be ridiculed, causing permanent psychological damage that could be avoided.